We addressed some of these electrostatics problems (Xray artefact like presence
of ions, crystal packing, etc) a long time ago. Feel free to look at:
Improving macromolecular electrostatics calculations.
Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
Protein Eng. 1999 Au
Hi Lu
Mosflm indexes your image using all defaults without any problems ;-)
XDS shouldn't have any difficulties with indexing this.
I suspect your crystal only diffracts to ~3.0 - 3.5 Å so you could do a better
experiment by moving the detector back to ~ 900mm...
BUT - PLEASE don't attach your
Edit your XDS.INP file to look like this:
!JOB= XYCORR INIT COLSPOT IDXREF
JOB=DEFPIX INTEGRATE CORRECT
Then rerun ads and be happy thereafter.
and RTFM !
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular
Hi LU,
the reason why IDXREF is not indexing smoothly is that the spot positions in
your SPOT.XDS are not very meaningful - you pick up a lot of noise! I plotted
your SPOT.XDS using
%%:-/tmp/luo% gnuplot
gnuplot> set size square
gnuplot> set out "tmp.png"
gnuplot> set term png nocrop medium si
Dear Jürgen and Lu,
I am not sure IDXREF found the correct solution (taken from IDXREF.LP):
* INDEXING OF OBSERVED SPOTS IN SPACE GROUP # 3 *
2372 OUT OF 40947 SPOTS INDEXED.
3 REJECTED REFLECTIONS (REASON: OVERLAP)
38572 REJECTED REFLECTIONS (REASON: TOO FAR FROM ID
Dear all,
I am trying to model a full-length double-domain protein in dimer. The
structure of both N and C terminal domains are known and the linker region
of 5 residues are present in both structure (the linker might be flexible
though). The N-terminal domain's structure is also a dimer, which ca
A 2-years postdoctoral position is available in the laboratory of Dr. Zhiyi Wei
at Department of Biology, South University of Science and Technology of China
(SUSTC, Shenzhen, China). Our research interests include signaling complexes
governing neuronal development (Mol Cell, 2011, 43; PNAS, 201
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Dear Xiao,
you would probably get started with molecular replacement to place one
domain after the other. Once you solved the structure you can use
external restraints to the known structures. If your resolution is
decent and the domains are not disor
